EcoCyc E. coli DatabaseEcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.
New to EcoCyc? Take the guided tour of the EcoCyc.org Web site, watch our free online instructional videos, or read our article in EcoSal (updated November 2018): "The EcoCyc Database".
EcoCyc User Guide >>
Cascade to the Rescue!
From protecting E. coli against phage infection to the promise of gene therapy: How does Cascade do it? Recent crystal structures of the enzyme are improving our understanding of this enzyme.Learn More
More than just K-12 MG1655
More than 500 E. coli strain databases are available via the change organism database link (upper right corner). They are less curated than EcoCyc but work with all our website tools, from Omics Dashboard to metabolic route search.
A quantitative metabolic model for E. coli K-12 derived from EcoCyc is available.Learn More
Maintaining the Outer Membrane
The 5-subunit Bam complex is responsible for the assembly and insertion of beta-barrel proteins into the OM of E. coli. Although a full understanding of its function in beta-barrel folding remains elusive, recent work has yielded many insights into subunit interaction and activity.
Metabolomics Data Analysis
Multiple tools are available in this website for metabolomics data analysis.Learn More
EcoCyc App is now BioCyc App
Have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster? Download the free BioCyc iPhone app to browse EcoCyc on the go! The NEW BioCyc app comes preloaded w/ EcoCyc.Download Here
Comparative Genome Analysis
Multiple comparative analysis tools are available in this website.Learn More
Gene Expression Data Analysis
Multiple tools are available in this website for analysis of gene expression data.Learn More
EcoCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:
- Genome browser and regulatory network browser
- Display of individual metabolic pathways, and of full metabolic maps
- Multiple omics data analysis methods for user-supplied omics and multi-omics datasets including the Omics Dashboard, painting onto pathway diagrams and metabolic maps, and tables of perturbed pathways
- Store groups of genes, metabolites, etc. in your account as SmartTables; share, analyze, transform those groups
- Metabolic route search tools
- Run metabolic models
- Comparative analysis tools
The E. coli Student Portal is a microbiology education site.
How to Cite EcoCyc
Please cite EcoCyc as Keseler et al. (2017), "EcoCyc: reflecting new knowledge about Escherichia coli K-12", Nucleic Acids Research 45:D543-50.
The development of EcoCyc is funded by NIH grant GM077678 from the NIH National Institute of General Medical Sciences.
The BioCyc webinar series introduces users to the basic and advanced features of the BioCyc website and the Pathway Tools software. A complete list of videos in additional download formats are available on the Video and Podcast page.
This video introduces the BioCyc.org site and the BioCyc collection of hundreds of Pathway/Genome Databases and covers:
- BioCyc site contents, including EcoCyc, MetaCyc, and our extensive database collection
- How to search, browse, and find what you need in the BioCyc collection
- How we represent metabolism, transcription, and all their parts